Contacts of the helix formed by residues 56 - 65 (chain A) in PDB entry 2A1X
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with GLU 56 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44A PHE* 6.5 0.4 - - - -
55A LEU* 1.3 77.3 - - + +
57A GLN* 1.3 56.6 + - - +
58A ARG* 3.0 6.5 - - - +
59A LYS* 3.3 21.2 + - + +
60A PHE* 3.2 20.3 + - - +
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Residues in contact with GLN 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A LEU 3.5 4.2 - - - +
54A THR* 3.2 31.4 - - + +
55A LEU* 3.0 37.3 - - + +
56A GLU* 1.3 78.5 + - - +
58A ARG* 1.3 57.9 + - - +
60A PHE* 3.6 10.5 - - + +
61A TYR* 3.1 23.4 + - - +
67A LEU* 4.0 27.2 - - + +
68A VAL 5.6 0.2 + - - -
69A ILE* 4.0 23.1 - - - +
142A TYR* 5.5 1.0 + - - -
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Residues in contact with ARG 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A PHE* 3.3 47.6 - - + +
47A THR* 3.1 47.1 + - + +
48A LEU 3.2 23.8 + - - -
49A ASP* 3.8 13.9 - - - +
50A ASN* 4.3 6.4 - - - +
54A THR* 3.0 33.0 - - + -
55A LEU 3.2 12.0 + - - +
56A GLU* 3.0 0.6 - - - -
57A GLN* 1.3 76.0 - - - +
59A LYS* 1.3 55.7 + - - +
61A TYR* 3.0 7.2 + - - +
62A GLU* 2.8 40.2 + - - +
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Residues in contact with LYS 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A PHE* 4.2 16.6 - - + -
56A GLU* 3.3 28.2 + - + +
58A ARG* 1.3 78.0 - - - +
60A PHE* 1.3 61.2 + - - +
62A GLU* 3.8 3.7 - - - +
63A GLU* 3.1 26.2 + - - +
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Residues in contact with PHE 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56A GLU* 3.2 8.3 + - - +
57A GLN* 3.6 19.1 - - + +
58A ARG 3.1 0.6 - - - -
59A LYS* 1.3 74.3 - - - +
61A TYR* 1.3 65.9 + - - +
62A GLU 3.2 0.3 + - - -
63A GLU 3.3 0.9 + - - -
64A ASN* 2.7 51.8 + - - +
66A PHE* 3.3 58.3 - + - -
67A LEU* 4.1 15.0 - - + -
68A VAL 5.5 0.7 - - - -
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Residues in contact with TYR 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A TYR* 3.8 28.3 - + + -
47A THR* 4.0 9.2 - - + -
57A GLN 3.1 10.7 + - - +
58A ARG* 3.0 12.4 + - - +
60A PHE* 1.3 78.2 - - - +
62A GLU* 1.3 58.6 + - - +
65A GLY* 2.6 45.9 + - - -
66A PHE* 3.6 20.9 - - - -
67A LEU* 3.8 10.5 - - + -
146A PHE* 3.3 37.5 - + - -
189A ILE 5.1 0.9 + - - -
190A VAL* 3.8 11.6 - - - +
213A HIS* 3.5 1.7 - - - -
257A PHE 3.5 20.4 - - - -
258A PHE* 3.3 5.5 - - - -
259A HIS* 3.2 31.2 + + + +
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Residues in contact with GLU 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A GLN 4.6 1.4 - - - -
44A PHE* 3.3 28.2 - - + +
45A GLN* 3.1 21.0 + - - +
46A TYR* 2.6 51.5 + - + +
47A THR* 3.2 12.8 + - - +
58A ARG 2.8 23.5 + - - +
59A LYS* 3.8 6.5 - - - +
61A TYR* 1.3 75.6 - - + +
63A GLU* 1.3 57.0 + - - +
213A HIS* 2.9 20.4 + - - -
214A LYS* 3.2 14.2 - - - -
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Residues in contact with GLU 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A LYS 3.1 17.8 + - - +
62A GLU* 1.3 75.3 - - - +
64A ASN* 1.3 70.0 + - - +
210A PRO 4.5 0.3 - - - -
211A GLY* 3.3 19.9 + - - -
213A HIS* 3.6 1.5 + - - -
214A LYS* 3.6 16.9 + - - +
243A LYS* 5.2 4.5 - - - +
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Residues in contact with ASN 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A PHE* 2.7 65.1 + - + +
63A GLU* 1.3 86.7 - - - +
65A GLY* 1.3 58.1 + - - +
66A PHE* 3.5 21.9 + - + +
210A PRO* 3.5 20.8 - - - +
211A GLY 2.9 20.0 + - - +
213A HIS* 3.3 6.2 - - - -
243A LYS* 5.3 2.6 - - - +
262A LEU* 3.4 14.2 - - - +
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Residues in contact with GLY 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A TYR* 2.6 33.6 + - - -
64A ASN* 1.3 72.6 - - - +
66A PHE* 1.3 56.8 + - - +
213A HIS* 3.1 26.4 + - - -
258A PHE* 3.3 5.2 - - - +
259A HIS* 3.1 28.8 + - - +
262A LEU* 3.9 5.2 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il